9.1. Epigenetics - methylation, histones

What is epigenetics?

The regulation and modification of genes that does not involve changes in the DNA sequence — from 'on top of' genes

What does epigenetics control?

Whether genes are switched on or off — it can change phenotype but not genotype

What factors can influence epigenetics?

Age, environment/lifestyle, and disease (e.g. cancer)

Why is epigenetics important for cell differentiation?

Activation and repression of genes dictates how cells terminally differentiate into skin, liver, brain cells etc.

What are the four types of epigenetics?

Histone modification, DNA methylation, non-coding RNA mediated gene silencing, and genomic imprinting

What is DNA methylation?

An epigenetic process where the cytosine base of DNA is chemically modified to 5-methyl-cytosine (5mC) to silence or repress gene expression

What enzymes catalyse DNA methylation?

DNA methyltransferases (DNMTs), which use S-adenosyl-methionine (SAM) as a methyl donor

What is the methyl donor in DNA methylation?

S-adenosyl-methionine (SAM)

In what DNA sequence context is 5mC found?

Only in CG dinucleotides — not in other contexts like CC, CA, or CT

What are CpG islands?

Regions of approximately 500-1000bp with high CG density compared to the wider genome, found in high concentrations in promoter regions and normally devoid of 5mC

How does CpG island methylation silence genes?

The methyl group physically prevents transcription factors from binding to the promoter region and activating gene expression

Where are CpG islands methylated in females?

On the inactive X chromosome

What happens when CpG island promoters of tumour suppressor genes are methylated in cancer?

They are constantly repressed, allowing tumour growth

What happens when DNA methylation is lost from tumour suppressor gene promoters?

Genes can be reactivated, causing cell cycle arrest and death of tumour cells

Why have DNMTs been pursued as drug targets?

Because inhibiting DNMTs could reactivate tumour suppressor genes in cancer

What happens to gene methylation during gamete and embryonic development?

Many active genes are later turned off (methylation) and many inactive genes are later turned on (demethylation)

What are the steps of DNA methylation maintenance during replication?

1) Methylated CG is replicated 2) New strand has unmethylated C (hemi-methylation) 3) DNMT methylates the new C to restore full methylation 4) Full methylation prevents inadvertent gene activation in subsequent replications

What is hemi-methylation?

When only one strand of replicated DNA has a methylated cytosine, before DNMT completes methylation of the new strand

What is passive DNA demethylation?

During replication, DNMT activity is reduced and hemi-methylation is maintained — over subsequent replications CpG islands remain unmethylated and the gene is slowly activated

What is active DNA demethylation?

The removal of the methyl group from cytosine through stepwise modification of 5mC via TET enzymes, followed by DNA repair enzymes

What is the stepwise pathway of active DNA demethylation?

5mC → 5hmC → 5fC → 5caC, completed by DNA repair enzymes

How does cancer alter DNA methylation?

Promoter hypermethylation silences tumour suppressor genes; hypomethylation of oncogenes drives cancer growth and survival

What is histone acetylation and what does it do?

The addition of acetyl groups to lysine residues on histones by HATs — opens chromatin and allows transcription factors to bind, promoting gene expression

What is histone deacetylation and what does it do?

The removal of acetyl groups from histones by HDACs — tightens chromatin and prevents transcription factor binding, repressing gene expression

What are histone acetyltransferases (HATs)?

Enzymes that add acetyl groups to lysine residues on histones, opening chromatin for gene expression

What are histone deacetylases (HDACs)?

Enzymes that remove acetyl groups from histones, tightening chromatin and repressing gene expression

How does acetylation affect histone charge and DNA binding?

It cancels the positive charge of histones, reducing their binding to DNA and exposing DNA for transcription factors

What are the four core histone proteins?

H2A, H2B, H3, and H4 — all can be acetylated at several lysine residues

What is histone methylation regulated by?

Histone methyltransferases (HMTs) and histone demethylases (HDMs)

What effect does histone methylation have on gene expression?

Depending on the type of methylation, it can lead to either gene expression or repression, causing variable changes between euchromatin and heterochromatin

What does histone phosphorylation do?

Reduces the positive charge of histones, opening chromatin and enabling transcription factors and DNA repair enzymes to bind

What is the role of histone phosphorylation in DNA damage?

During double-stranded breaks, H2A and H2A.X are phosphorylated, recruiting DNA repair enzymes and increasing accessibility of the break to repair proteins

What reverses histone phosphorylation?

Phosphatases

What is histone ADP-ribosylation?

The addition of ADP-ribose to glutamate and arginine residues on histones by ADP ribosyl transferases, adding negative charge and relaxing chromatin (euchromatin)

What reverses histone ADP-ribosylation?

ADP-ribose-protein hydrolases

When does histone ADP-ribosylation occur?

In response to DNA damage

What is histone SUMOylation/ubiquitylation?

The addition of small ubiquitin-like molecules (SUMO, ≤100 amino acids) or ubiquitin (76 amino acids) to lysine residues on histones

What three enzymes are involved in SUMOylation/ubiquitylation?

E1-activating enzyme, E2-conjugating enzyme, and E3-ligating enzyme

What reverses SUMOylation/ubiquitylation?

Isopeptidases

What is the role of SUMOylation/ubiquitylation in gene expression?

Unclear — the exact role in gene expression is not yet fully understood

What is euchromatin?

Loosely packed histones associated with active gene expression

What is heterochromatin?

Tightly packed histones associated with gene repression

What is the genome?

All the genetic information of an organism, encoded in DNA, involved in gene expression, replication, inheritance, and evolutionary modifications